Comments/Advice Please

Hi,
Regarding going to Kanazawa by bullet train, you can leave from Tokyo Stn., but why not just get on the bullet train at the JR Ueno Station?
And then for going to Odawara, it is your choice of course. But for the same amount of time with a good connection, you can get from Matsumoto to Odawara as you can to Nagoya. And it'd be then an extra 2 hours by bullet train to get from Nagoya to Odawara. Only you can decide if it is worth it really, I would suggest not wasting the time and spending it more at your destination. And it's unclear what would hold your attention in Odawara for 3 full days.....
Please be aware also that you will be arriving in Japan during Golden Week (Apr. 29-May 6) which is one of the busiest holiday times of the year. Many places will have a lot more people than usual. Leaving Tokyo should not be a problem though since at the time you're leaving, most people will be returning to Tokyo.
While you are missing the cherry blossom season, you will though be just in time for wisteria season, and if you have the time, you can see a stunning display of them at the Ashikaga Flower Park just north of Tokyo:

http://goo.gl/EvSI3v

For Kanazawa, be sure to see the Kenrokuen Garden - it is rated as Japan's most beautiful traditional and historical garden.
I'd suggest though that 3 days are enough to see Tokyo. Some other day trips would add more variety. Popular choices are Nikko, Kamakura/Enoshima, and Hakone. If not using your JR Pass, look into a regional pass for them:

http://www.japan-guide.com/e/e2357.html

For going to/from Tokyo, the Keisei is 1 choice but there are also cheaper ways by bus:

http://accessnarita.jp/en/home/